Reflection

Laura Terada Week 3 Journal

Reflection

Overall, do you think this paper was clearly written? Why or why not?

I thought the paper was overall clear. I was able to understand the introduction and the materials methods section easily. The subheadings in the results section also helped, and it served as a general outline of the paper. The only confusing part was that the paper discussed many different genes from different studies; however, the figures and tables helped to clarify the comparisons between the different datasets.

Based on what is written in the methods section, do you think you could reproduce their experiments and data analysis?

Yes- the authors gave a very detailed description of their culture parameters and which programs they used for data analysis.

What else would you like to know about their methods, results, and future directions?

I would like to know how this study could be used to analyze posttranscriptional modes of cellular regulation and what changes would need to be made or what other factors would need to be considered. Moreover, what exactly accounts for the differences in results between the batch cultures versus chemostat cultures? Is the only difference the fact that one is a more controlled environment? Also, are there different phases of long-term low temperature exposure/acclimation? Lastly, I would like to know how can these results on acclimation for yeast relate to more complex organisms.

Kevin McKay Week 11 Journal

I thought it was clearly written, as clearly as it could be. There was so much in this paper including 4 separate experiments that they referred too and lots of genes and transcription factors so I thought it was clear for how much work they did although overall I found it messy as a whole.

If I knew what they were talking about through most of the analyzation methods I could probably reproduce the experiment.

I would like to know what lead them to choose the specific growth rate of 0.03/h in the batch culture experiments they based theirs off of. I would like to know more about the programs they used or analyzation. Also more about the function of the 259 genes that were consistently differentiated in regulation during adaptation in the three batch studies would be good. Maybe some more on how they plan to combat the effects of changing cultivation parameters without impacting others.

James P. McDonald Week 11 Journal

I think the paper was written fairly clearly. The paper contains some complicated methods of data collection and analyses but it was as clear as it could have been in dealing with such topics.

Based on what is written in the methods section, do you think you could reproduce their experiments and data analysis?

The paper contained a somewhat in depth methods section so I do think I could recreate the experiment but maybe not to great accuracy. I have not performed experiments like this before, especially from the data analysis perspective so it would not be easy at first. But since it was explained rather clearly I think I may be able to do it with their guidance.

What else would you like to know about their methods, results, and future directions?

I know that they wanted to eliminate a specific growth rate in their study to compare it to batch cultures but I was wondering if they had to make it anaerobic to do this. It seems that the lack of oxygen in their study caused discrepancies in their comparison to the batch cultures. Is their a way to make a closer comparison and eliminate this factor? Another thing I would like to know is what would happen at even lower temperatures than were tested. Would the same trend continue or would something else happen to its transcriptional regulation? Due to the difference between a gradual temperature decline and a cold shock I would be interested to see what would happen if the temperature continued to decline slowly. Would the yeast eventually enter a state that would correlate with the cold shock effect? This could be a possible future direction to take the study.

Matthew E. Jurek Week 11

In terms of clarity, I thought this paper was OK. The results section was rather large and the subheadings helped. However, I felt things could have been better organized. Also, the discussion of various genes became confusing. Sometimes examples of certain genes were stated and other times not. The large number of genes paired with inconsistent examples was somewhat confusing.

Based on what is written in the methods section, do you think you could reproduce their experiments and data analysis?

The methods section is straight forward. However, at the end of the growth conditions section it is mentioned that several factors were constant for at least 3 volume changes before sampling. These volume changes were never stated. It would still be possible to recreate, but maybe not identically. I also don't know if I could work through the statistically testing even thought the equation is provided.

What else would you like to know about their methods, results, and future directions?

By the end of the paper it was clear that batch cultures were not appropriate for studies like these. However, in the discussion it is stated that the batch culture results are needed for comparison in order to fully understand which genes are impacted by the cold temp. I would assume previously published batch results will be used for as long as possible. If these results ever do not address specific genes, would they perform a batch culture experiment followed by a chemostat experiment for comparison purposes? This was a thought I had regarding future directions.

Anthony J. Wavrin Week 11 Journal

I think the paper was very clear overall. The information that is described is very thorough and uses a lot of references. It is evident that they are doing a lot of work and comparisons. The only unclear part is that overall result. Instead, they come up with a lot of minute conclusions about a lot of things but, the y do not do a good job of wrapping it all up into 1 coherent message.

Based on what is written in the methods section, do you think you could reproduce their experiments and data analysis?

Due to my lack of expertise in this field, I do not think I could reproduce their experiment and data analysis. I think the actual experiment could be replicated using the sources they cited in the materials and methods. I think the data analysis would be very difficult to try to replicate because they just cite programs and one equation.

What else would you like to know about their methods, results, and future directions?

I think the one thing I would like to know is their overall result. They concluded many things from this study, it seems it was much more work in analysis rather than actually conducting the experiment, but the ideas seemed very unorganized and all over the place. I am interested to see what direction they went into after this paper because, that would probably be a pretty good indicator of the most important finding in this study.